The gastrointestinal tract is the most densely colonized region of the human body (Savage, Ann. Rev. Microbiol. 31, 107 (1977); Tannock, Normal microflora (Chapman and Hall, London 1995)) and the accumulated evidence indicates that this collection of microbes has a powerful influence on the host in which it resides. Comparisons between germ free and conventional animals have shown that many biochemical, physiological and immunological functions are influenced by the presence of the diverse and metabolically active bacterial community residing in the gastrointestinal tract (Marteau and Rambaud, FEMS Microbiol. Rev. 12, 207 (1993); Norin et al., Appl. Environ. Microbiol. 74, 1850 (1991); Tannock, supra). Lactobacilli are important residents of the microflora (Ahrne et al., J. Appl. Microbiol. 85, 88 (1998); Kimura et al., Appl. Environ. Microbiol. 63, 3394 (1997)), and have been the subject of intense and growing interest because of their possible role in the maintenance of gastrointestinal health (Bengmark, Gut 42, 2 (1998)). Of immense importance to lactobacilli functioning in this role is the ability to endure in the harsh conditions of the gastrointestinal tract, where the gastric pH frequently falls below 2.0 in healthy individuals (McLauchlan et al., Gut 30, 573 (1998)).
The identification of conditionally expressed genes provides a wealth of insight into the physiological consequences of and responses to a given stimulus. In the case of Lactobacillus acidophilus, a significant challenge has been in understanding the intestinal roles and activities of this organism. An important element in this regard is the determination of which characteristics are important for the survival and success of this organism in the gastrointestinal tract. While differential display (Liang and Pardee, Science 257, 967 (1992); Welsh et al., Nucleic Acids Res. 20, 4965 (1992)) has been used extensively to identify conditionally expressed genes in eukaryotes, the application of this methodology in prokaryotes has not been explored to a comparatively significant extent (Abu Kwaik and Pederson, Mol. Microbiol. 21, 543 (1996); Fislage, Electrophoresis 19, 613 (1998); Fislage et al., Nucleic Acids Res. 25, 1830 (1997); Wong and McClelland, Proc. Natl. Acad. Sci. USA 91, 639 (1994); Zhang and Normark, Science 273, 1234 (1996)). Some of the practical problems in employing these methods in prokaryotes include the relatively large proportion of structural RNA species in the total RNA, the low level of polyadenylation of mRNA (Sarkar, Ann. Rev. Biochem. 66, 173 (1997)), which prohibits the use of 3′ dT anchored primers and the structural instability and short half life of low abundance mRNA species of prokaryotes as compared to eukaryotes (Higgins et al., Curr. Opin. Genet. Dev. 2:739 (1992)).
The present invention contributes to the art by providing promoters as compositions and for use in methods of expressing nucleic acids in a variety of conditions.